Scientist, Protein Bioinformatics

Key Skills

Bioinformatics, Data Modeling, Data pipelines, Machine learning techniques, Nextflow, Public Health, Python Programming, Snakemake

Job Description

A Bit About Us:

We are Arcadia Science. Arcadia is a science company founded and led by scientists. Our mission is to transform evolutionary innovations into real-world solutions by openly developing more efficient, replicable, and sustainable ways to leverage the biology of diverse organisms. Scientists at Arcadia share as much of their research as possible to gather community feedback and accelerate scientific progress.

The Opportunity:

We are looking for an innovative and collaborative scientist to join the Functional Annotation team, where we employ comparative biology to study proteins across diverse organisms and unlock biological novelty. As part of Arcadia’s Discovery Platform, our team explores evolutionary patterns at the molecular scale by conceiving and crafting new methods, tools, and analyses using cutting edge biology and technology.

In this role, you will engage collaboratively with a multidisciplinary team to design, create, and iterate on user-focused workflows and tools for comparing protein families in diverse organisms. Your role will be to help us enhance our current computational functionality by refining existing structure-based protein comparison tools and by developing and deploying new expansions aimed at comparative protein biology. Enthusiasm for and participation in open science is also required as we routinely share our findings via our open source Pubs and GitHub.

Our ideal candidate should have deep knowledge of protein biology and state of the art tools for computationally studying proteins (think AlphaFold, Foldseek, docking tools, molecular dynamics, etc). Additionally, they should have computational expertise and experience with statistical analysis. If this sounds like you, please review the responsibilities and requirements below and consider submitting your application.

• Responsibilities:
• Develop and apply computational pipelines and statistical methodologies for comparing protein structures and other features across diverse organisms
• Work collaboratively with scientists across Arcadia to design and iterate on computational tools aimed at comparative biology of proteins
• Communicate with scientists who have different levels of technical expertise
• Help design figures and write fully open access pubs

Education/Experience:

• PhD in biochemistry, biophysics, computational biology, bioinformatics, or related field, or equivalent experience

Biological

• Deep knowledge about protein function, biology, structure, and biophysics
• Experience with homology modeling, docking, or molecular dynamics
• Experience with computational structural biology; we don’t anticipate experimental solutions but prefer prior experience in this process
• Familiarity with AlphaFold, ESMFold, etc.
• Synthesize ideas, data, and findings into fully open-access pubs and engage with the scientific community to maximize impact and garner feedback that improves the work

Computational

• Expertise in at least one programming language (Python preferred), with a willingness to adapt and learn new languages as needed
• Experience with open-source software and contributing to open-source projects
• Experience developing scalable bioinformatics pipelines
• Experience with statistical analysis and modeling
• Experience with a workflow manager (eg Snakemake or Nextflow) is a plus
• Machine learning and modeling is a plus

Other

• Ability to quickly generate customized protein structure figures and videos
• Written and oral communication skills and a willingness to share research openly, early and often

Interested applicants should send a resume and a one-page cover letter which includes a brief narrative of your professional background, highlighting accomplishments in protein-based computational projects, and a description of what you could bring to the team.

The expected salary range is $125,000-$175,000 per year with generous equity and benefits, depending on experience level. The scientist will be part of the functional annotation team, and will report to Brae Bigge. The position will require the individual to be on-site at our Berkeley, California headquarters.

Arcadia Science is an equal opportunity workplace; we welcome people from all backgrounds and communities. We provide competitive compensation and practical benefits to keep you happy and healthy so that you can do your best work. Please note that an offer of employment from Arcadia is contingent upon the successful clearance of a reference and background check.